The War of Gotham
by princebejitasama
Summary: Magneto, the Mutant Master of Magnetism, unleashes his forces upon a recovering Gotham in the wake of Protocol 10. His goal; to capture a high profile project undertaken by WayneTech. Closely watching the pro-mutant terrorist, the X-Men follow his progress. Meanwhile, Batman deals with the resurrection of his greatest foe.


[A/N: As stated, this is a crossover between Marvel and DC Comics, taking place in everybody's favourite city, Gotham. This story is altogether AU, although several canon aspects are mentioned throughout. Some of these include the events of Arkham City, the events of the Avengers and intermingled canon from the comics, cartoon and movies of the X-Men and Amazing Spiderman series.

The main players of this story will be Batman (AC Verse), Magneto (Movie Verse) and Wolverine (Comic/Movie Verse), with supporting roles being provided by The Joker (AC Verse), Venom (Comic/AU Verse), Sabretooth (Movie/AU Verse), and Rorschach (Watchmen, AU Verse). All of these characters have been somewhat edited to fit all their stories in together, but aspects of the characters' true personality have not been changed. If these characters rub you the wrong way or ruin the story for you, I make no apologies.

This story is a big one, and a lot of brains have contributed to the first several chapters. I'd love to hear any and all remarks, praise, criticisms and suggestions as to my writing, as long as it is constructive, and not just "this sucks because you used movie version of Magneto".]

The War of Gotham

_(DC/Marvel Crossover)_

Chapter One: New Beginnings

_-"Lazarus Rising"-_

It hadn't taken long for crime to spring up in Gotham after what could best be described as the Arkham Disaster. Even though most of the inmates of the super prison had been either killed or shipped off to other maximum security prisons across America, a number of Gotham's baddest had slipped under the radar, making their escapes through the network of sewers below the city streets, and fleeing beyond the sight of the GCPD. Attempts had been made by Commissioner Gordon to apprehend the runaways, but thus far, only a handful of the gaudy numbers had been brought to justice. One of these escapees was undoubtedly the most dangerous man to ever set foot in Gotham City; A man who had been presumed dead, but was apparently alive and well.

The Joker.

During the rebuilding process following in the wake of Protocol 10, the body of the maniacal jester had been recovered from the rubble. There was no time to rejoice at the fall of the clown criminal, though, as alarms were raised the morning after his corpse was transported to Gotham Hospital. The coroner had been found dead in the dingy morgue, with his throat slashed, eyes gouged out, and a single playing card pinned to his forehead with a scalpel. No leads could be found by any one (even the Dark Knight failed to trace the psychopath), and the Joker vanished into the shadows along with the countless others.

In the weeks following the Joker's disappearance, a string of bizarre murders had sprung up across the city. Each victim was found with twisted grins of laughter etched into their faces (although the glassy stare of death failed to steal the sheer terror from their eyes), and joker cards littered the crime scenes. Gotham's Clown Prince of Crime continued to elude capture, though, as the trail was always long cold before the Police or the Bat arrived on the scene.

Until now.

Atop the PD, Jim Gordon strode swiftly across the rooftop, clutching a folder under an arm, holding a silver lighter in one hand and cupping it with another, the flames licking at the cigarette clenched between his teeth. With quick strides, he ascended the stairs towards the building's highest point, and flipped the switch on the obsidian steel Bat Signal. Powerful lamps flickered brightly, then glared into life, painting the easily recognisable sign of the Batman across the cloudy night skies. "C'mon... Hurry it up..." he growled under his breath, dragging heavily on his cigarette while the spotlight called for the caped vigilante's aid.

On the East Side of Gotham, the Batmobile roared through the streets. The Pits were stirring trouble with the East-West Gang again, and once more, innocent civilians had been caught in the crossfire. The small GCPD force who had arrived to break up the skirmish looked to be on the verge of becoming overrun, but the Batman's intervention had brought a close to the fighting. Two people had died (in his own mind, Bruce Wayne felt responsible for the deaths, because he hadn't gotten there in time) and while the culprits were on their way to the station, it wasn't enough. Crime kept flooding into his city like an evolving disease; Cure one person, ten more became ill.

Gotham. He hated this city as much as he loved it some times.

"Bruce, eyes up." The familiar female voice crackled into life through his inbuilt communications, and he immediately knew what Barbara Gordon was contacting him about. He leaned forwards and glanced up to the sky. Sure enough, his suspicions were correct. The call.

"I see it, Oracle." He replied, taking a sharp right turn and zipping along an alleyway towards the GCPD Main. "I'm on the way."

"Be careful out there."

The Batman smirked. "Careful isn't really a concept I understand anymore."

Jim Gordon's pale face and the large number of cigarette butts littering the ground around the spotlight told the Batman this was indeed an emergency. The last time he'd seen the Commissioner like this was when he'd informed the Dark Knight about the Joker's return from apparent death. As he dropped down from the radio tower atop the PD, Bruce silently prayed that this had nothing to do with the Clown Prince.

"Sure took your damn time getting here." Gordon muttered, turning to face the masked man as his booted feet hit the ground.

The Bat ignored the jibe, emerging from the shadows. "What happened, Jim?" he asked, voice like sharp gravel.

"The Clown. Again." He confirmed Bruce's fears. "But this time, it's not chasing ghosts. We've got a lead." Gordon slipped a hand inside his trench coat and pulled out the folder, handing it over to the vigilante. "CCTV at Gotham West-Main Pharmaceuticals captured this just over an hour ago."

Inside the folder were several photographs. Despite the hazy quality of the printouts, there was no mistaking that pale skin, violet suit and shock of green hair. Batman's blood boiled at the sight of the Joker's maniacal grin. "Gotham West-Main Pharmaceuticals." he muttered under his breath, snapping the folder shut and handing it back to Gordon.

"Yeah." Gordon turned his back, pacing towards the spotlight. "Sent a team out about fifteen minutes ago. They haven't found anything tangible yet, but they haven't got your eyes. Just-" But when Gordon turned back around, he was alone on the rooftop, and in the distance, the screech of tires filled the air as the Batman sped towards West Main Avenue.

One hour previously, the Joker stood over the bound and gagged form of yet another victim to be. A trio of thugs dressed in sideshow attire carried boxes of goods from an inner store room out across the lobby towards a white van parked at the curb. Grinning like a lunatic, the clown leaned down towards the man behind the counter, barely containing his laughter. "Oh, don't be so glum!" he cooed, patting the man gently on the cheek. "You're serving a higher purpose here! Why, you're going to lead him straight to me!" He ripped the tape off the man's mouth, and the hapless employee of Gotham West-Main Pharmaceuticals screamed in terror.

"You'll wake the dead with that racket, sonny jim!" The lunatic clown pulled a single capsule from his pocket, holding it between his thumb and forefinger. "Now, open wide! Here comes the airplane!" He grabbed the man by the chin, forcing his mouth open, then rammed the capsule down his throat. "There's a good lad! Eat up!" His smile became more twisted, his voice lowering to a gravelly growl. "It's good for what ails ya." Shooting a final grin at the camera, he placed his usual calling card on the choking man's chest. "Pack it up boys! Time's a wastin'!" His insane laughter as he strolled from the building mixed with that of the man he'd just sentenced to a needless death. Despite the crippling and agonising pain, the man would die laughing. And, in the Joker's mind, that was the best death to be had. Why, he was practically doing this town a service! No one laughed any more! But he'd fix that, alright. He'd fix this town, one violent murder after another.

Emergency vehicles crowded the street by the time Bruce arrived on the scene. From his vantage point atop an adjacent water tower, the Batman could see police officers marking exclusion zones with blue and white tape. He could see Jack Ryder's sharp profile as he spoke to his camera crew, gesturing in exaggerated fashion towards the building. Pulling his grapple gun from his belt, the vigilante took careful aim towards an overhead exhaust vent and squeezed the trigger. His cape fluttered out behind him as he swung across the divide, scrambling into the vent and slipping inside.

Batman wound his way down the stairwell, his ears picking up the echo of voices in the lobby. "I want every white van in a twelve mile radius flagged down and inspected!" That, no doubt, was Bullock. Bruce felt a pang of annoyance crawl up his spine at the sound of the pompous detective's voice. Bracing himself, he pushed open the fire door and strode across the room.

"You won't find him that way." He announced, his keen eyes sweeping the room as the cowl's in built scanners displayed the lobby in bright infra-red. "The Joker's too smart to be caught by you so easily. He's undoubtedly already ditched the van."

"Hey! Who let him in here?!" Bullock growled, gesturing angrily towards the caped vigilante. "This is a crime scene, Batman. No one's allowed in here aside from GCPD and emergency services!"

"Thanks for the information." Bruce had extreme difficulty hiding his grin.

The cowl's HUD couldn't pick up any kind of evidence trails to follow, so he deactivated the scanner, sweeping across the room to find something out of place, ignoring the wide eyes following his progress. "I mean it." Bullock sneered. "Get outta here, or I'll arrest you for interfering with police investigations. Last warning."

"Noted." Kneeling, he activated a small flash light on his wrist and peered beneath a nearby cabinet, looking for... There. He slid his fingers beneath the cabinet, pulling out what looked like a transaction receipt for the sale of a derelict mannequin factory in the industrial district of Gotham South. The buyer's signature was an untidy scrawl in green ink, but Bruce could make out the name of Joseph Kerr in the scribble.

"You can't just take evidence from a crime scene!" Bullock bellowed like a wounded bull, storming towards the Bat. "That's it, I'm taking you down to the station."

"No need, detective. I was just leaving." The Batman replied with a smile, dropping the bill of sale into Bullock's hands. Without sparing the officer a final glance, he strode from the room and out the side door, levelling his grapple gun at a nearby building and zooming off into the skies. "Oracle." He pressed a finger to his ear as he alighted the brickwork. "I need you to run a check for any of Joker's usual aliases. He's recently bought up an old factory in the industrial district, and I've got a hunch he's collected more real estate than just one dilapidated building."

"Already on it." Oracle replied coolly. "What do you think he's up to?"

"Trouble." Closing the line, he took off at a sprint, leaping from the rooftop. He dropped a few feet before his cape opened out behind him. In the near distance, the booming growl of the Batmobile's engines roared into life, and rounding a corner, Bruce dropped like a stone directly into the driver's seat. "The worst kind of trouble." he muttered to himself.

Bruce Wayne's assumptions had been correct. As he wound his way through the industrial sector's empty streets, Oracle called through with the information Batman had been looking for. "Two warehouses near the docks sold to Jack White, the old Water Board building leased to Joseph Kerr... Yeah, this doesn't look good Batman..." she'd said hurriedly. "He's got direct access to the water supply and the sewers, not to mention the docks."

"Don't worry, Oracle. Whatever he's up to, I'll stop it." Making a sharp turn, the Batman took his vehicle off the main road and into an old utility alley running adjacent to the factory, killing the engine.

"I'll let you know if I hear anything. GCPD channels are still quiet; Bullock doesn't seem to have made the connection yet."

"Figures."

Much to Bruce's surprise, he found the building completely unguarded from the outside. "Just what are you up to?" he muttered, narrowing his eyes at the factory. He had expected a well lit area, complete with sniper-toting sentries and side show thugs patrolling the perimeter. Aside from the obvious lack of defences, Bruce also noted that there was no sign of the white van (or any other car or vehicle for that matter) either coming or going from the lot. _"Odd... If I didn't know him, I'd almost think that Joker set up a false trail for me to follow..." _He thought to himself. But of course, the Joker never set false trails. Every crime he committed was, invariably, to attract the Batman's attention.

When he arrived inside the dim and dusty factory, his suspicions that the clown had led him astray were proved unfounded. As the door slammed closed behind him, a pale white figure sprang from the shadows, arms raised, cackling with insane mirth, painted face grinning from ear to ear. With his greater than usual human reflexes, Bruce swung a gauntleted fist towards the figure, and the head was separated from the body, tumbling backwards down the corridor, the mannequin rocking back and forth on it's spring.

"Did I scare ya, Bats?! No?! Good! Would have hated myself if you got guano all over that handsome cape of yours!" The Joker's lunatic voice cackled from the crackling speaker attached to the dummy's chest. Gritting his teeth in a silent snarl, Bruce stepped past the mannequin, progressing along the shabby hallway. As he stepped into the reception area, a television screen flickered into life, and the Joker grinned down from the wall behind the desk. "So glad you could make it!" he laughed, clapping his hands together. "Been meaning to have a little chat with you ever since that little bit of unpleasantness in Arkham City! You know, shake hands, kiss and make up, bygones being bygones and that sort of thing. When you get a moment, pop on out to the factory floor! I've got a proposition for you!" With nothing left to do, the Batman pushed through the doors and strode down another bare corridor, then entered the main floor. Floodlights boomed on overhead, and Bruce's eyes swept the room.

Odd assortments of furniture littered the area, making the production floor look something like the attic of a crazy old cat lady. Several mannequins stood sentry around the hall, some dressed in similar attire to the joker, while a few hanging from the rafters looked suspiciously like Batman himself. His gaze found the centre of the room, and lounging lazily in a red felt throne, was the Joker.

"Batty! Bats, my _oldest_ of friends!" he roared, leaping from the chair, practically skipping towards the vigilante, spreading his arms in a greeting of warmest welcome. "_So_ _good_ to see ya! How've you been keeping?! You're looking fit! New suit?! You know, I was starting to think you didn't want to see m-"

Bruce immediately seized him by his jacket and slammed him into a wooden support beam hard enough to crack the timber. "You're supposed to be _dead_!" He growled, grip tightening. "How did you survive?"

The Joker took a moment to regain his breath, waving a hand airily while a breathless chuckle escaped his lips "Oh come now Bats, you know me! Fit as a horse! Constitution of an elephant! Slept it off like a bad hangover! You'd be surprised what a healthy 40 winks can accomplish!"

Frustration rose up in Bruce Wayne, and he slammed his fists into Joker's collar bones. "I'm not playing your games, Joker." he said quietly, eyes boring into the clown's. "You obviously called me for a reason. What do you want?"

"That's all I get?" The Joker asked in a simpering, mock hurt voice while a frown crossed his face. "It's been weeks, Batty..._ Weeks_! You haven't called, you haven't written... Could have been dead for all I know! And all I get is "What do you want"?" He shook his head, making a 'tsk'ing sound. "Goodness, are my feelings _hurt_!" His laughter was cut off by another powerful shove, and he grunted in pain. "Oh, fine then! Don't play along! You always were such a bore! Straight to business it is... But first, do you mind letting me go? This suit cost me a _fortune_!"

Batman obliged by tossing the clown across the room, sending him crashing through an old cabinet, scattering mannequin limbs in all directions. "You've been buying up real estate with access to the waterways lately. I want to know why." he demanded.

Rising from the debris, Joker placed a steadying hand on his forehead, releasing a low groan. "Haven't figured that one out for yourself yet?" he asked. "I thought that would have been _quite_ obvious."

In honesty, it didn't take a genius to figure it out. "You're poisoning the town again."

"Well... Yes and no..." the Joker shrugged his shoulders non-committally. "I know what you're thinking... 'What _is _it with this guy and _poisons_?! Doesn't he ever learn anything _new_?!' Well my answer is that the oldest jokes never stop being funny!"he cackled. "But yes, whether or not I proceed with my wondrous little plan... That all depends on you, really. See, I have a job that needs doing,and I'm far too busy to take care of it myself."

"The day I work with scum like you will be a cold day in Hell." the Bat growled, his knuckles audibly cracking as he clenched his fists.

"Not even to save your beloved Gotham?" The Joker arched a brow, settling himself back in his throne. "It's rather simple, my old pal; You take care of this _itsy bitsy teeny weeny _task for me, and I won't kill every single person in a forty mile radius. You reject my offer, or try to lock me up, or pass on my plans to that insufferable Police Commissioner buddy of yours... Well, the Gothamites will be quenching their thirsts on a cocktail of Titan Formula and Joker Toxin." The longest pause of all followed the statement. "All up to you, Bats."

The Dark Knight had been backed into a corner. With no choice available to him, Bruce hung his head, admitting defeat. "Tell me what you want, Joker." he muttered in gravelly tones.

A slow smile spread into a wide grin across the Joker's face. "That wasn't so hard, was it?" The Joker tittered. His grin began to fade. "I want you to find out where Harley Quinn is hiding. Find her, and give me an address."

Bruce blinked in confusion, raising his head. "Harley?" he repeated. Whatever he'd been expecting, it hadn't been this. "Why are you looking for Harley Quinn? I thought she was your most loyal servant."

"She _was_..." The Joker muttered in icy tones. "After Protocol 10, she disappeared into the woodwork like the filthy little rat she is with a truckload of cash and half of my best men!"

"Why? Why would she do something like that?"

"It doesn't matter why!" Joker snarled, slamming a fist onto the arm of his chair. "The conniving little whore stabbed me in the back! She _must_ pay the price!"

"And if I find her... What happens then?"

"You tell me where she is, I go and collect her, and I give her a taste of my utmost dissatisfaction... After that, you 'n me can go back to hounding each other like always! Cross my heart and hope to die." he finished, drawing an 'x' across his chest.

"How can I trust you?" The Batman asked, narrowing his eyes. "How do I know that once you get what you want, you won't just proceed with your plan to poison the city?"

"That's the beauty of it, Bats." The Joker grinned. "You don't really have an option."

_-"The Golden Opportunity"-_

New York's streets rang with cheering and applause. Streamers and confetti filled the air, brass bands blared out an echoing fanfare, the soldiers and servicemen of the U.S. Army waved to the people lining the streets, lapping up the admiration of the people they'd saved.

The threat of Loki and the Chitauri had been defeated by the Avengers Initiative, and the world was once again safe. Or, so it would seem.

On a raised platform at the parade's finishing point, several suited men stood in waiting for the procession to end. High-ranking military heads, members of the Presidential cabinet, and a heroic figure bedecked in the Stars and Stripes. "Ladies and Gentlemen, may I have your attention please?" That was the President himself, speaking through the booming PA. At the request, the music died down, the cheering faded away to a dull chatter, camera flashes blinking and winking from across the crowd, and the man ran his fingers through his hair, briefly shuffling his speech. "Once again, the United States of America has been faced with insurmountable odds. Once again, the United States of America stands triumphant in the face of overwhelming foes." A loud cheer rose up from the thronging crowds. "Without the efforts of the U.S. Army and S.H.I.E.L.D, none of us would be standing here today. Our thanks go out to those brave men and women who made the ultimate sacrifice in the defence of this beautiful nation. A moment's silence for the fallen, if you please."

Immediately, silence fell. Heads were bowed, as the respectful moment was observed by the populace. "A further thanks must be given, fellow Americans." the President stepped back up to the podium. "Thanks, to a man who almost single-handedly organised the defence of not just New York, but the entire planet itself. The man I speak of is the ultimate personification of the American Dream, a man who bleeds red white and blue. You know him, as Captain America." The loudest cheer of all rose from the masses, and the streets echoed with the sound of applause, stamping feet and bellowed cries of praise and respect, as Steve Rogers made his way to the podium, raising an acknowledging hand to the adoring people of New York. "For his bravery in the fight with the invaders, it is with the utmost privilege that I award Captain Steven Rogers with the Medal of Honour, for bravery and valour beyond the call of duty."

The resulting blast of applause was deafening. There was, however, one man in the entirety of New York that wasn't happy about the successes of Captain America. This man was standing at the window of a ritzy hotel room overlooking the parade, gazing down on proceedings with disdainful eyes.

Erik Lehnsherr, known to the X-Men as Magneto, had been looking to capitalise on the Chitauri's attack. He had been banking on the Avengers failing, and at the time of the attack, had been poised to swoop in with the Brotherhood of Mutants and clean up the scraps. Both S.H.I.E.L.D and Loki, along with his army of extraterrestrial soldiers, would have been eradicated, and the masses of advanced alien technology (including the Tesseract) would have fallen into his hands. At first, the world would have thanked and praised his efforts, and slowly, mutants would have been admired rather than scorned. Lehnsherr, though, had a severe hatred of human kind, stemming from his early life in the concentration camps of Nazi Germany and witnessing the atrocities inflicted upon mutant kind. With the Chitauri's technology in his hands, Magneto would have created a world where humans lived in servitude and misery.

But now, thanks to Captain America and the Avengers, the bulk of the Chitauri's weapons and technology had either been destroyed or was in the hands of the U.S Government, which meant the same thing; It was useless to Magneto. He'd considered the possibility of gathering his forces and launching an assault on the Pentagon, but his numbers were insufficient for such an undertaking. More and more mutants passed through the doors of Charles Xavier's Academy for Gifted Youngsters each and every day. And Charles refused to see reason in that regard. No, Erik Lehnsherr needed to bide his time.

As the President pinned the medal to Captain America's chest, the crowd below gave a resounding cheer, and Magneto scooped up the wine glass on the window sill, having no further interest in watching the proceedings. He lowered himself into an elegant arm chair, and with a glance, summoned a metallic table to his side. After depositing his glass, he lifted the newspaper, and was met with the headline "_Captain America Saves New York_", heading a photograph of the patriotic legend.

Fantastic, yet another reminder. Hastily turning the page, his eyes found another article, which grabbed his attention much more than the tribute to the Avengers. "_WayneTech Nearing __Completion of $20billion Satellite Program_".

Magneto's brows knitted together. "Interesting..." he muttered, allowing his gaze to wander down across the section.

_ After four long years, Bruce Wayne's highly secretive satellite project is nearing completion, according to WayneTech gurus. Little is known about this program, but snippets released by the Gotham based conglomerate suggest that the aptly nick-named 'WayneWeb' will reshape our views on technology as we know it._

_ "I can't say too much about the project, other than that everyone from the President down will benefit from it," said company CEO, Bruce Wayne, in a press conference earlier in the week. Furthermore, he stated that "it will change the face of telecommunications on a global scale"._

_ Rumours and gossip indicate that Wayne's brain baby could potentially include functions such as global wireless internet access, aerial surveillance, war time defensive parameters, television & radio access, environmental aid, and a vast array of other services (full list of possibles, probables and long shots on page 4)."You'll be blown away, I guarantee it," Wayne stated, upon closing the meeting._

_ The general public, however, will need to patiently wait until the heads of WayneTech release the system's full capabilities. If any of WayneTech's prior releases are anything to go by, this could potentially be the biggest forward step for telecommunications since Sir Isaac Newton decided to fly his kite in a thunder storm. This reporter will wait with baited breath._

Suddenly, Magneto's mind was abuzz with possibilities. A highly advanced satellite array, placed in the heavens by one of the greatest minds of the twenty-first century, beaming down upon the entire planet. In the hands of a criminal mastermind like Erik Lehnsherr... Well, the "WayneWeb" could be an extremely powerful weapon.

An old (and failed) plan flitted across his memory. A plan involving a highly advanced program called Cerebro. The device, when utilised by Charles Xavier, allowed him to pinpoint the location of mutants all across the globe. William Stryker had tried to use the machine to _destroy_ all mutant life, rather than find them.

With WayneTech's satellite program, Magneto could potentially turn that same plan back onto human kind, obliterating them all in one foul swoop without any mutant casualties. A smile finally worked its way onto Erik's face.

This was a big task, though. He would need Mystique with him, and the likes of Toad, Juggernaut and Pyro would also be necessities. But he couldn't have too many footsoldiers from the Brotherhood holidaying in Gotham, or else he'd rouse the suspicion of the X-Men, perhaps even S.H.I.E.L.D. No, he would need to call in outside help. And more than one person.

First on his list would be Victor Creed. Sabretooth would work any job, as long as he was offered the right amount of money. But who else could he call in, aside from the feral half-brother of Wolverine? Not a decision to be made rashly, he decided. He would sleep on it, and act once he'd had time to sum up his options.

Rising from his chair, Magneto neatly folded the paper and placed it on the table, scooping up his glass of wine, and made his way back to the window. Down below, Captain America was shaking hands with the President, while the crowd roared tumultuously. Raising the glass in a mock salute, Erik Lehnsherr smiled down on the hero. "Your good health, Captain."


End file.
